The Living Dead

By studying the microscopic bacteria that bloom on our bodies after we die, scientists hope to unlock surprising mysteries of the departed.

CreditIllustration by Louise Zergaeng Pomeroy

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By Peter Andrey Smith

Jan. 18, 2016

The bright aseptic room smelled of Pine-Sol and bleach and overripe Camembert. A white-bearded man lay on a stainless-steel examination table, his face angled toward the skylight and the cold, cloudless morning. An investigator read from his clipboard: 61-year-old white male discharged from a Detroit hospital last night was found at home, shirtless, in a wheelchair, a .38-caliber handgun in his right hand. On his chest was a burn that appeared to be an exact match of the gun’s barrel. Carl Schmidt, the medical examiner, wiped the contact wound with a wet sponge.

“If we’re lucky, it exited,” he said.

Two technicians hefted the body onto its side.

“And . . . let’s look at the other side.”

The skin was mottled where the blood had begun to settle, but his back had no open wounds.

“We’re going to have to extract the bullet.” Schmidt paused. “Next.”

He had seven more bodies to inspect. By his account, it had been a typical night. Schmidt and his team — a pathology fellow, a medical student and three autopsy technicians — moved over to examine two pedestrian fatalities struck down when a vehicle jumped a curb. Schmidt felt around their skulls for fractures. Another man with a history of cardiovascular disease had been found at the bottom of a stairwell; and an elderly woman, her body bag marked “decomp,” had lain alone for several days, undiscovered. The most perplexing case was a 27-year-old woman who was found dead in a city park with a USB phone-charging cable tied around her arm, the victim of an overdose. “She was out shooting drugs in a park on a Saturday night with a frost warning?” Schmidt asked, a roundabout way of suggesting she might have overdosed before being dumped outside. Though she was unidentified, she had one thing in common with the other bodies: The exact time of death was unknown and practically unknowable.

Schmidt, a soft-featured, 58-year-old pathologist (or, as he put it, “a balding, fat white guy”), has served as the chief medical examiner for Wayne County, which includes Detroit, one of the nation’s busiest morgues, for 13 years. When I visited in October, his office had handled more than 2,800 bodies that year, 1,900 of which involved autopsies. Autopsy reports provide a basis for legal and criminal investigations, and limitations in their findings contribute to why about a third of murders nationwide never lead to an arrest.

That Sunday morning, Schmidt snapped on two pairs of purple gloves and pulled on a Tyvek suit. Before he autopsied one pedestrian, Schmidt swirled a sterile cotton-tipped applicator in an ear of the victim, snapping off the tip into a plastic container, then swabbed her nose, mouth and belly button. An autopsy technician cut a quarter sphere into her skull with an electric saw, pulled off the cap and rolled another swab over the cross-section of the bone. “See right there?” Schmidt said. “The reason we do this is the head is probably the most sterile place of the body.” He pointed to the dark fissure separating the brain’s hemispheres, a region he expected to serve as a negative control for the experimental analysis. “This is ideal because the head is far away from the viscera, which are teeming with bugs.”

No problem in forensic science has been investigated more, and understood less, than the post-mortem interval. Medical investigators calculate the interval between death and the discovery of a body using three cardinal measurements: temperature (algor mortis), stiffness (rigor mortis) and the settling of blood (livor mortis). These factors vary depending on a person’s distribution of visceral fat, as well as their clothing, the ambient air temperature and other factors. After two days or so, though, these observations are no longer trustworthy. Schmidt keeps a copy of a statistical opus on post-mortem intervals, in which Claus Henssge and his co-authors warn against extrapolating much beyond 48 hours, but he takes an even more pessimistic view. “Post-mortem interval is one of the most pseudoscientific bits of information out there that, and I hate to use this, will never die.”

Medical examiners can often deduce cause of death based on an autopsy, but the exact time of death is hard to determine. At best, this evidence comes from an attending physician or, lacking that, an eyewitness. “But let’s say that a body was dumped in an alley or one of Detroit’s many empty lots,” Schmidt said. “And that’s all you know about the case. Let’s say it’s August and it’s 90 degrees. And the body is flaccid and lividity is fixed. So, has that body been there for less than 24 hours or more than 24 hours? The answer is: Who knows?”

Which was why Schmidt had teamed up with a group of scientists — Heather Jordan, a microbiologist in Mississippi; and Eric Benbow and Jennifer Pechal, two entomologists in Michigan — to systematically swab bodies during routine death investigations. They hoped to gather testimony from an unusual set of witnesses: the microbes that live after we die.

The swabbing in Detroit, which began in 2014 and quickly won a grant of nearly $850,000 from the National Institute of Justice, is the largest sustained effort to sample microbes from human cadavers. Informally known as the Human Postmortem Microbiome project, it arose out of a national crisis in forensic science, one that legal advocates and researchers have pieced together over the past decade. In 2004, Michael Saks and Jonathan Koehler, legal scholars at Arizona State University and Northwestern University, respectively, reviewed 86 cases in which DNA evidence exonerated the wrongfully convicted and found that forensic error across many types of analyses — fingerprinting, microscopic hair comparison, blood-spatter — was second only to faulty eyewitness accounts in obtaining convictions that were later overturned. In a 2013 research paper, legal scholars reviewed capital rape-and-murder cases from the 1980s and extrapolated that the justice system produced at least 33,000 false felony convictions annually.

The crisis came to the fore in 2009, with a widely cited report from the National Research Council, an arm of the National Academies of Sciences, Engineering and Medicine, that found nearly all aspects of forensic science wanting. Crime labs often used tools invented by law enforcement, including ballistic and bite-mark analyses. Some techniques had never been scientifically validated and lacked enforceable standards. Judicial review, the report said, could not cure the infirmities of forensic science. “That’s why the N.A.S. report called for the creation of a national institute of forensic science,” Saks told me. “Because it had no faith in the institution of forensic science, it had no faith in academic institutions, it had no faith in the courts.”

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Dr. Carl Schmidt in his office, in 2011.CreditJeff Kowalsky

Benbow, a researcher at Michigan State University, was among those galvanized by the report. Trained as a field biologist, he studied insect-metamorphoses patterns in graduate school and eventually used the same techniques to measure insect growth in death investigations. Flies often arrive within minutes after a death to mate and lay eggs. The phase of development to pupae typically range from 5 to 11 days. (The warmer the air and soil, the faster blowflies grow.) He soon came to recognize some of the field’s shortcomings: Experts presented plausible hypotheses about the time it took for insects to colonize a body and arrived at a consensus, but sometimes the statistical models hinged on small samples. As a result, expert witnesses were hard pressed to state their “confidence intervals,” which refers to the probability of any given estimate’s accuracy. “You can disagree about how you got to that estimate,” Benbow said. “But having a confidence interval is what’s going to be important. That’s kind of the holy grail of forensic pathology.” Investigators use estimated time of death, in part, to exclude or implicate a suspect. Post-mortem intervals have played a key role in many trials. Benbow’s mentor, for instance, once gave testimony regarding the estimated time of insect colonization that helped overturn a conviction in a case that precipitated the abolition of the death penalty in Canada.

In 2010, Benbow began analyzing three pairs of donated human remains deposited at a body farm in San Marcos, Tex., an outdoor facility dedicated to the study of decomposition. Around the same time, he and his colleagues were finding that microbes altered the rate at which flies were lured to a body. They also realized that by studying microbial successions — the sequence in which the microbial communities proliferate over time — they could further narrow the window of death and arrive at more confident estimates. The necrobiome, as Benbow called it, represented all the organisms involved in decomposition: bacteria and fungi and nematodes, blow flies and flesh flies, rodents and vertebrate scavengers. After Benbow presented the concept at a 2014 meeting of forensic scientists in Seattle, Schmidt told him he worked about an hour away from his lab and could provide swabs from about 3,200 bodies a year.

Much like the research on the microbiome has fundamentally reshaped our understanding of biology, studies of the necrobiome appear poised to illustrate, on a small scale, what many hope will be a more rigorous way of doing forensic science. Micro-organisms living in the body migrate and adapt almost immediately to the lack of oxygen and the breakdown of the immune system. The sequence is rapid: Bacteria infiltrate the liver within 20 hours and spread to the heart and other organs in less than 58 hours. Anaerobic bacteria in the intestine can double in less than 10 minutes and eventually cede their territory to oxygen-loving organisms when the stomach ruptures. Because these successions appear to be highly predictable, microbes function as timekeepers and trace evidence. Death may stop one biological clock, but another one keeps ticking.

The origins of the Human Postmortem Microbiome project actually began 10 years earlier, when Heather Jordan traveled to southern Ghana. She was part of a six-member team studying the so-called mystery disease, a skin-eating bacterial infection caused by Mycobacterium ulcerans, which can lead to lifelong disfiguration. Scientists have long suspected that insects transmit the disease, and the team wore chest-waders in the blistering heat as they cast nets in slow-moving backwaters, collecting insects and preserving them in alcohol. It was during this trip that Jordan began speaking with Benbow, who was part of the team. By then he had tapped into a small but devoted group of forensic entomologists studying bugs found on dead bodies.

Jordan, who is now a microbiologist at Mississippi State University, had never witnessed an autopsy or visited a crime scene and had given little thought to the nuances of putrefaction. “I knew that those guys were in forensics,” Jordan told me. “That’s all I knew.” But she felt she had a personal stake in the matter. Around the time of her Ghana trip, her older brother died from a suspected alcohol overdose. By the time her family found his body, nearly a month later, Jordan could not recognize his face; there was almost no way of determining it was her brother. In the years leading up to their collaboration with the Human Postmortem Microbiome, she began sending Benbow book-length emails. Just as microbes played a role in transmitting disease, she suspected they had to have something to do with decomposition. Jordan said she asked Benbow whether anyone had used microbes in determining the time of death and whether they could do a controlled experiment along those lines. Jordan told me, “Pretty much that all came about from me thinking, ‘What can we do?’ ”

Scientists still need better empirical evidence before turning any plausible hypotheses into courtroom testimony. Already, however, an initial methodology in the Human Postmortem Microbiome project can at least produce an estimate for a minimum post-mortem interval. In 2014, Benbow and Pechal went to a vacant lot where there was the body of a suspected homicide. They had a well-established time of death and, after swabbing the body, they compared it with cases in Detroit with similar post-mortem intervals. It was only a single data point, but the relative abundance of microbes looked remarkably similar.

Biologists now suspect that opportunistic micro-organisms that feed on corpses persist in trace quantities everywhere on earth. But when a person dies, the body begins to digest itself, and these mysterious organisms rapidly emerge and assemble on decomposing mammal flesh. (The microbiologist Jack Gilbert compares them to shore-bound pirates, lying in wait for the next shipwreck.) This hypothesis draws largely from a detailed study led by Jessica Metcalf, a biologist at the University of Colorado, Boulder, who late last year confirmed that communities of the same bacteria, fungi and other eukaryotes bloomed at regular intervals after death, like a microbial clock. In dead mice and in donated human remains, under varying soil conditions and across a range of temperature fluctuations, the model predicted time of death accurately across experiments.

Awareness of the necrobiome is increasing. The medical examiner’s office in Honolulu, by matching and dating samples taken from a deceased person’s skin with the microbes on their phones and remote controls, is currently trying to see whether microbial DNA can act like fingerprints. Jordan, meanwhile, has extended her lab’s research into the post-mortem interval at the molecular level. She speculated that as predictable patterns emerge from these microbial communities, they might also find more specific indicators of microbial activity, findings that would then allow researchers to build field-detection kits that pinpoint time of death and were as easy to use as a pregnancy test. “All we need is one light out of all of the background of stuff that’s going on, out of all the craziness, all we need is one clear light that’s reproducible,” Jordan said.

A 35-millimeter film scanner whirred through black-and-white negatives in October, as Schmidt sat in a histology lab, inspecting a box full of swabs. He had heard about a few intriguing findings: His scientific collaborators — Jordan, Benbow and Pechal — could identify a victim’s gender by the microbial patterns (potentially useful for burn victims) and isolate which part of the body had been swabbed. Drug deaths appeared to harbor distinct communities of microbes compared with deaths by natural causes. For all Schmidt knew, the body he suspected of being dumped in the park might carry traces of the location where she last injected drugs. He was most intrigued by the apparent differences between homicides and suicides, which could stem from the chronic depression that preceded a suicide or the sudden spike in adrenaline in the moments before a homicide. The victim of a homicide more often receives medical care at a hospital before dying than does someone who commits suicide, and Schmidt suspected bacterial differences might be an artifact. Which made the first case he inspected, the 61-year-old man who shot himself, a potential outlier: Here was a suicide in a recently discharged hospital patient.

Schmidt had doubts they would find anything resembling an infallible post-mortem interval but thought even a minor improvement worth pursuing. “I suppose part of what’s driving this is there’s information out there that we’re missing,” he said. “One of the things that forensic pathology has to do over the next few years is to find other ways to expand its reach, other than the traditional bullet-pulling, quantification-of-injuries whodunit as you see on TV.”

Later that week, he planned to drive to Benbow and Pechal’s lab to deliver the swab samples. Schmidt began his graduate training as neurobiologist, and he loved studying the brain. He was eager to know more about the moment when the relative sterility within our skulls is breached by organisms contributing to our decay. Bodies found decomposing for days often contained intact hearts and lungs and discernible livers and kidneys. “You open the skull and the brain has turned into pea soup,” he said. “It’s remarkable. You often find in people, even when their abdominal organs are recognizable, that the brain has liquefied. What drives that?”

Schmidt slipped the last of the swabs into a specimen bag. His investigation had only just begun, and the implications are already profound: Beyond our last breaths, beyond the complete cessation of brain function, some intimate truths about us — what we once ate, the drugs and medications we once took, the homes and hospitals we once visited — seem to persist in our microbes. Can we learn to decipher what they have to tell us?